4.6 Article

Recognition of quinolone antibiotics by the multidrug efflux transporter MexB of Pseudomonas aeruginosa

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Molecular Mechanism for the Allosteric Inhibition of the Human Serotonin Transporter by Antidepressant Escitalopram

Weiwei Xue et al.

Summary: This study explored the allosteric modulation mechanism of hSERT using two MD simulation strategies. The results showed that escitalopram enhanced its binding to the orthosteric site by binding to the allosteric site. Additionally, escitalopram occupying the allosteric site also blocked its dissociation from the orthosteric site. A new conformational coupling between extracellular and intracellular salt bridges was also identified. These findings are important for understanding the allosteric modulations of not only hSERT but also other clinically important therapeutic targets.

ACS CHEMICAL NEUROSCIENCE (2022)

Article Infectious Diseases

Diversity detected in commensals at host and farm level reveals implications for national antimicrobial resistance surveillance programmes

Tanya J. Laird et al.

Summary: Phenotypic and genotypic heterogeneity of AMR traits in bacteria from animal populations pose a barrier to correct interpretation of AMR surveillance data, highlighting the need for a more in-depth sampling model.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2022)

Article Multidisciplinary Sciences

AB-DB: Force-Field parameters, MD trajectories, QM-based data, and Descriptors of Antimicrobials

Silvia Gervasoni et al.

Summary: Antibiotic resistance poses a major threat to public health, and the development of chemo-informatic tools for designing antibacterial libraries is urgently needed. AB-DB is an open database that provides comprehensive information on antimicrobial compounds, including force-field parameters, molecular dynamics trajectories, quantum-mechanical properties, and curated physico-chemical descriptors. These reliable and non-trivial properties facilitate data mining and statistical analysis in the discovery of new antimicrobials.

SCIENTIFIC DATA (2022)

Review Chemistry, Multidisciplinary

Structural and Functional Diversity of Resistance-Nodulation-Cell Division Transporters

Philip A. Klenotic et al.

Summary: Multidrug resistant bacteria pose a global threat, making common infections increasingly difficult to eradicate. Research has shown that bacterial membrane proteins belonging to the resistance-nodulation-cell division superfamily play crucial roles in bacterial resistance to antibiotics. Studies have reviewed the assembly and function of bacterial inner membrane pumps, providing insights for the design and optimization of new efflux pump inhibitors to better treat difficult-to-cure infections.

CHEMICAL REVIEWS (2021)

Article Microbiology

Predictive Rules of Efflux Inhibition and Avoidance in Pseudomonas aeruginosa

Jitender Mehla et al.

Summary: Efflux pump avoidance and inhibition are crucial properties for optimizing antibacterial activities against Gram-negative bacteria. This study identified molecular determinants and predictive models that can help researchers discover and optimize antibacterial agents suitable for treating P. aeruginosa infections. The developed predictive models are based on physicochemical predictors such as molecular shape, amphiphilicity, aromaticity, and partition coefficient, which can be applied to compounds with unrelated chemical scaffolds.
Review Chemistry, Multidisciplinary

Multidrug Efflux Pumps and the Two-Faced Janus of Substrates and Inhibitors

Helen Zgurskaya et al.

Summary: Antibiotics are effective against infectious bacterial diseases, but antibiotic-resistant bacteria present a challenge to modern medicine. Gram-negative bacteria, with their outer membrane acting as a permeability barrier, rely on active efflux and low permeability to resist antibiotics. Efforts to overcome this resistance include enhancing antibiotic penetration and inhibiting efflux pumps, offering potential for novel therapeutic strategies.

ACCOUNTS OF CHEMICAL RESEARCH (2021)

Article Multidisciplinary Sciences

Structural and functional analysis of the promiscuous AcrB and AdeB efflux pumps suggests different drug binding mechanisms

Alina Ornik-Cha et al.

Summary: This study reveals the structure and drug-binding mechanism of the AdeB subunit of the Acinetobacter baumannii AdeABC efflux pump, as well as its differences with the Escherichia coli AcrB. The research shows that these efflux pumps can provide a deeper understanding of antibiotics and drug resistance.

NATURE COMMUNICATIONS (2021)

Article Biochemistry & Molecular Biology

Understanding the Polypharmacological Profiles of Triple Reuptake Inhibitors by Molecular Simulation

Gao Tu et al.

Summary: This study analyzed the selective binding modes of different TRIs to human monoamine transporters based on the simulated structure of hSERT, identifying key residues contributing to binding selectivity. The findings offer important insights for the rational design of a single drug with better polypharmacological profiles targeting multiple receptors.

ACS CHEMICAL NEUROSCIENCE (2021)

Review Chemistry, Multidisciplinary

Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria

Ilyas Alav et al.

Summary: Tripartite efflux pumps and related type 1 secretion systems in Gram-negative organisms exhibit diverse functions, energization, and structural organization. This review highlights the role of periplasmic adaptor proteins (PAPs) in providing a common architectural scaffold and proposes a new integrated model of PAP-mediated communication within these systems.

CHEMICAL REVIEWS (2021)

Article Immunology

Expression of RND efflux pumps mediated antibiotic resistance in Pseudomonas aeruginosa clinical strains

Abed Zahedi Bialvaei et al.

Summary: The study identified that clinical isolates of Pseudomonas aeruginosa commonly express RND efflux pumps, leading to antibiotic resistance. Overexpression of mexB and mexY in ICU wards was significantly prevalent in the studied strains, correlating with resistance to most anti-pseudomonal antibiotics.

MICROBIAL PATHOGENESIS (2021)

Article Biochemistry & Molecular Biology

Molecular Mechanics Study of Flow and Surface Influence in Ligand-Protein Association

Shivansh Kaushik et al.

Summary: This study investigated the molecular association processes under different environments, finding that additional ligand transporting forces and intermolecular interactions between the ligand and environmental objects can affect the association rate and processes. The research sheds light on the effects of the solvent flow and surface environment on ligand-protein associations and provides insights for experimental design.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

Review Microbiology

Bacterial efflux transporters' polyspecificity-a gift and a curse?

Helen Zgurskaya et al.

Summary: This article reviews the mechanisms underlying the biochemical versatility of RND transporters in reducing intracellular accumulation of toxins and antibiotics. The discussion also touches on the implications of the polyspecificity of RND transporters for bacterial survival and the development of efflux pump inhibitors effective in clinics.

CURRENT OPINION IN MICROBIOLOGY (2021)

Article Chemistry, Medicinal

AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings

Jerome Eberhardt et al.

Summary: AutoDock Vina is a widely used open-source program for molecular docking with new features such as support for macrocycles and explicit water molecules. The latest version also includes support for AutoDock4.2 scoring function, simultaneous docking of multiple ligands, and a batch mode for docking a large number of ligands. Python bindings have been implemented to facilitate scripting and workflow development.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

Article Chemistry, Multidisciplinary

GNINA 1.0: molecular docking with deep learning

Andrew T. McNutt et al.

Summary: Molecular docking software Gnina 1.0, utilizing convolutional neural networks as scoring functions, outperforms AutoDock Vina in redocking and cross-docking tasks when binding pockets are explicitly defined. The ensemble of CNNs shows good generalization to unseen proteins and ligands, producing scores that correlate well with known binding poses. The 1.0 version of GNINA is available under an open source license for use as a molecular docking tool.

JOURNAL OF CHEMINFORMATICS (2021)

Review Microbiology

Fighting Antibiotic Resistance in Hospital-Acquired Infections: Current State and Emerging Technologies in Disease Prevention, Diagnostics and Therapy

Ekaterina Avershina et al.

Summary: Antibiotic resistance is a growing global threat that may result in more deaths than all cancers combined by 2050. Research is focused on the current state of antibiotic resistance, emerging technologies, and strategies for preventing the spread of infectious diseases.

FRONTIERS IN MICROBIOLOGY (2021)

Review Multidisciplinary Sciences

AcrB: a mean, keen, drug efflux machine

Jessica Kobylka et al.

ANNALS OF THE NEW YORK ACADEMY OF SCIENCES (2020)

Article Biochemistry & Molecular Biology

Binding and Transport of Carboxylated Drugs by the Multidrug Transporter AcrB

Heng-Keat Tam et al.

JOURNAL OF MOLECULAR BIOLOGY (2020)

Article Chemistry, Physical

Molecular Interactions of Cephalosporins with the Deep Binding Pocket of the RND Transporter AcrB

Alessio Atzori et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2019)

Article Multidisciplinary Sciences

Structures of the wild-type MexAB-OprM tripartite pump reveal its complex formation and drug efflux mechanism

Kenta Tsutsumi et al.

NATURE COMMUNICATIONS (2019)

Article Chemistry, Physical

Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations

Emilia P. Barros et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)

Review Biotechnology & Applied Microbiology

Antibiotic resistance in Pseudomonas aeruginosa: mechanisms and alternative therapeutic strategies

Zheng Pang et al.

BIOTECHNOLOGY ADVANCES (2019)

Review Infectious Diseases

Epidemiology and Mechanisms of Resistance of Extensively Drug Resistant Gram-Negative Bacteria

Emily M. Eichenberger et al.

ANTIBIOTICS-BASEL (2019)

Article Multidisciplinary Sciences

Crystal structures of multidrug efflux pump MexB bound with high-molecular-mass compounds

Keisuke Sakurai et al.

SCIENTIFIC REPORTS (2019)

Article Biochemistry & Molecular Biology

Improvements to the APBS biomolecular solvation software suite

Elizabeth Jurrus et al.

PROTEIN SCIENCE (2018)

Article Biochemistry & Molecular Biology

Water-mediated interactions enable smooth substrate transport in a bacterial efflux pump

Attilio Vittorio Vargiu et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2018)

Article Biochemical Research Methods

NGL viewer: web-based molecular graphics for large complexes

Alexander S. Rose et al.

BIOINFORMATICS (2018)

Review Microbiology

Multidrug efflux pumps: structure, function and regulation

Dijun Du et al.

NATURE REVIEWS MICROBIOLOGY (2018)

Article Microbiology

Computer simulations of the activity of RND efflux pumps

Attilio Vittorio Vargiu et al.

RESEARCH IN MICROBIOLOGY (2018)

Article Microbiology

RND transporters in the living world

Hiroshi Nikaido

RESEARCH IN MICROBIOLOGY (2018)

Article Multidisciplinary Sciences

Multiple entry pathways within the efflux transporter AcrB contribute to multidrug recognition

Martijn Zwama et al.

NATURE COMMUNICATIONS (2018)

Review Chemistry, Medicinal

Recent updates of fluoroquinolones as antibacterial agents

Hend A. A. Ezelarab et al.

ARCHIV DER PHARMAZIE (2018)

Article Biochemistry & Molecular Biology

Switch Loop Flexibility Affects Substrate Transport of the AcrB Efflux Pump

Reinke T. Mueller et al.

JOURNAL OF MOLECULAR BIOLOGY (2017)

Article Multidisciplinary Sciences

Transport of lipophilic carboxylates is mediated by transmembrane helix 2 in multidrug transporter AcrB

Christine Oswald et al.

NATURE COMMUNICATIONS (2016)

Review Biotechnology & Applied Microbiology

Mechanisms of Antimicrobial Resistance in ESKAPE Pathogens

Sirijan Santajit et al.

BIOMED RESEARCH INTERNATIONAL (2016)

Article Chemistry, Physical

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

James A. Maier et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Review Microbiology

Structural basis of RND-type multidrug exporters

Akihito Yamaguchi et al.

FRONTIERS IN MICROBIOLOGY (2015)

Review Chemistry, Physical

Molecular Recognition and Ligand Association

Riccardo Baron et al.

ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 64 (2013)

Article Multidisciplinary Sciences

Structural basis for the inhibition of bacterial multidrug exporters

Ryosuke Nakashima et al.

NATURE (2013)

Article Multidisciplinary Sciences

Multidrug binding properties of the AcrB efflux pump characterized by molecular dynamics simulations

Attilio V. Vargiu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop

Thomas Eicher et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket

Ryosuke Nakashima et al.

NATURE (2011)

Article Multidisciplinary Sciences

Mechanism of recognition of compounds of diverse structures by the multidrug efflux pump AcrB of Escherichia coli

Yumiko Takatsuka et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemical Research Methods

PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes

Timothy V. Pyrkov et al.

BIOINFORMATICS (2009)

Article Chemistry, Multidisciplinary

AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility

Garrett M. Morris et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Article Biochemistry & Molecular Biology

Crystal Structure of the Multidrug Exporter MexB from Pseudomonas aeruginosa

Gaby Sennhauser et al.

JOURNAL OF MOLECULAR BIOLOGY (2009)

Article Chemistry, Analytical

Determination of pKa values of active pharmaceutical ingredients

Sandra Babic et al.

TRAC-TRENDS IN ANALYTICAL CHEMISTRY (2007)

Review Chemistry, Physical

Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms

Jianyin Shao et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)

Article Biochemistry & Molecular Biology

Complementarity of hydrophobic properties in ATP-protein binding: A new criterion to rank docking solutions

Timothy V. Pyrkov et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

Drug export pathway of multidrug exporter AcrB revealed by DARPin inhibitors

Gaby Sennhauser et al.

PLOS BIOLOGY (2007)

Review Biochemistry & Molecular Biology

Molecular lipophilicity in protein modeling and drug design

Roman G. Efremov et al.

CURRENT MEDICINAL CHEMISTRY (2007)

Article Multidisciplinary Sciences

Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism

Markus A. Seeger et al.

SCIENCE (2006)